chr10-99528007-G-A

Position:

• chr10-99528007-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_120618.1(LINC01475):​n.376C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 152,748 control chromosomes in the GnomAD database, including 20,944 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.52 (20885 hom., cov: 34)
  • Exomes 𝑓: 0.43 (59 hom.)
• Consequence: LINC01475 NR_120618.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152

Genes affected

(HGNC:):

LINC01475 (HGNC:51113): (long intergenic non-protein coding RNA 1475)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01475	NR_120618.1	n.376C>T		non_coding_transcript_exon_variant	3/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000452494.2	n.271G>A		non_coding_transcript_exon_variant	2/2	1
LINC01475	ENST00000548010.1	n.376C>T		non_coding_transcript_exon_variant	3/5	1

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79428 AN: 151930 Hom.: 20863 Cov.: 34

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.504

GnomAD4 exome AF: 0.431 AC: 302 AN: 700 Hom.: 59 Cov.: 0 AF XY: 0.425 AC XY: 169 AN XY: 398

Gnomad4 AFR exome AF: 0.607

Gnomad4 AMR exome AF: 0.400

Gnomad4 ASJ exome AF: 0.444

Gnomad4 EAS exome AF: 0.486

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.410

Gnomad4 NFE exome AF: 0.412

Gnomad4 OTH exome AF: 0.480

GnomAD4 genome AF: 0.523 AC: 79491 AN: 152048 Hom.: 20885 Cov.: 34 AF XY: 0.525 AC XY: 38997 AN XY: 74330

Gnomad4 AFR AF: 0.513

Gnomad4 AMR AF: 0.565

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.627

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.500

Alfa AF: 0.515 Hom.: 39897

Bravo AF: 0.524

Asia WGS AF: 0.598 AC: 2082 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.5
DANN	Benign	0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10883365; hg19: chr10-101287764;